Research workbench
Crystal structure of the cbs domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and S-adenosyl-L- methionine.
Analyse Crystal structure of the cbs domain pair of protein MJ0100 in complex with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KPD
- Type
- protein
- Length
- 478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ0100
- UniProt
- Q57564
- Ligands
- MTA, SAM
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Uncharacterized protein MJ0100 | protein | 119 | 31% helix, 26% strand | Q57564 |
| B | Uncharacterized protein MJ0100 | protein | 121 | 36% helix, 25% strand | Q57564 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 5 copies · chains A, C, D
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.74 | 0.81 | 76 | SAM, MTA |
| 2 | 831 | 0.71 | 0.77 | 72 | MTA |
| 3 | 371 | 0.67 | 0.81 | 40 | empty |
| 4 | 199 | 0.60 | 0.82 | 29 | empty |
| 5 | 65 | 0.38 | 0.78 | 13 | MTA |
Interfaces
4 interfaces between chains.
- B–C · 1533 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 698 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 596 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KPD · Crystal Structure of the CBS domain pair of protein MJ0100 in complex with 5… · the same entry in another collection · chain D against D, TM-score 1.00
- Q57564 · AlphaFold monomer V2.0 prediction for L-aspartate semialdehyde sulfurtransferase (Q57564) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q57564
- Elsewhere: RCSB PDB 3KPD · PDBe 3KPD · UniProt Q57564
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